how to keep an internal drive from being mounted on startup?

First of course insure that you deselect and reselect the SSD

And yes SSDs act different and do seem to cause confusion with OS X boot routine

Mark volumes to be ignored by TimeMachine. If that doesn't work then you need to troubleshoot that and find why or what is corrupt like remove the existing preference files.

If you clear nvram in any means then you have to reset the default startup disk.

depending, your SSD may just need to be format and restored, and always be ready and have a clone of your SSD, a sparse disk image maybe but always have a 2nd boot drive volume. And that it has the latest firmware.

The problem is that when I do dismount them, they disappear from the Time Machine (and Spotlight) Ignore list. Is that normal?

No. Launch the Terminal application in any of the following ways:

☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)

☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.

☞ Open LaunchPad. Click Utilities, then Terminal in the icon grid.

Triple-click the line below to select it, then drag or copy the text — do not type it — into the Terminal window and press return:

mdutil -s -a

Some lines of output should appear below what you entered, showing the Spotlight indexing of each volume and AFP sharepoint. Is indexing of the volumes in question enabled or disabled?

Is there any way to find a log of what exactly the machine is doing on bootup to see what it may be doing before it boots from the SSD?

If you have more than one user account, these instructions must be carried out as an administrator.

Launch the Console application in any of the following ways:

☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)

☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.

☞ Open LaunchPad. Click Utilities, then Console in the icon grid.

Step 1

Make sure the title of the Console window is All Messages. If it isn't, select All Messages from the SYSTEM LOG QUERIES menu on the left.

Enter "BOOT_TIME" (without the quotes) in the search box. Note the timestamps of those log messages, which refer to the times when the system was booted. Now clear the search box and scroll back in the log to the last boot time when you had the problem. Post the messages logged after the boot, during the time something abnormal was happening.

For example, if the problem is a slow startup taking three minutes, post the messages timestamped within three minutes after the boot time, not before. Please include the BOOT_TIME message at the beginning of the log extract.

Post the log text, please, not a screenshot. If there are runs of repeated messages, post only one example of each. Don’t post many repetitions of the same message. When posting a log extract, be selective. In most cases, a few dozen lines are more than enough.

Please do not indiscriminately dump thousands of lines from the log into a message.

Important: Some private information, such as your name, may appear in the log. Edit it out by search-and-replace in a text editor before posting.

Step 2

Still in Console, look under System Diagnostic Reports for crash or panic logs, and post the entire contents of the most recent one, if any. In the interest of privacy, I suggest you edit out the “Anonymous UUID,” a long string of letters, numbers, and dashes in the header of the report, if present (it may not be.) Please don’t post shutdownStall, spin, or hang logs — they're very long and not helpful.

That log extract starts at 10:16:09 with the BOOT_TIME message, and ends at 10:18:25. You seem to have gotten to the login window 6 seconds after booting, so I can't reconcile that information with your report, unless something was happening before the BOOT_TIME message.

You're running a lot of third-party system modifications, any of which could be contributing to your problem: outdated versions of Parallels and Little Snitch, MySQL, DenyHosts (which is incompatible with 10.8), damaged installations of the Cisco VPN client and of NETGEARGenie, and iStat.

Your system, in other words, is too heavily modified to be maintainable. You can't expect stability or good performance from that configuration.

I suggest you remove as many of those modifications as you can live without, according to the developers' instructions. Update or fix the ones you can't live without. Maybe you'll see some improvement.

The fact that software is commercial doesn't mean that it's of good quality or that it can't cause conflicts. A large part of the traffic on this site is generated in just that way.

Any third-party software that doesn't install by drag-and-drop into the Applications folder, and uninstall by drag-and-drop to the Trash, is a system modification.

Whenever you remove system modifications, they must be removed completely, and the only way to do that is to use the uninstallation tool, if any, provided by the developers, or to follow their instructions. If the software has been incompletely removed, you may have to re-download or even reinstall it in order to finish the job.

Here are some general guidelines. Suppose you want to remove something called “BrickYourMac.” First, consult the product's Help menu, if there is one, for instructions. Finding none there, look on the developer's website, say www.brickyourmac.com. (That may not be the actual name of the site; if necessary, search the Web for the product name.) If you don’t find anything on the website or in your search, email the developer. While you're waiting for a response, download BrickYourMac.dmg and open it. There may be an application in there such as “Uninstall BrickYourMac.” If not, open “BrickYourMac.pkg” and look for an Uninstall button.

You may have to log out or reboot in order to complete an uninstallation.

If you can’t remove software in any other way, you’ll have to erase your boot volume and perform a clean reinstallation of OS X. Never install any third-party software unless you're sure you know how to uninstall it; otherwise you may create problems that are very hard to solve.

Trying to remove complex system modifications by hunting for files by name often will not work and may make the problem worse. The same goes for "utilities" that purport to remove software.

Search for those terms on this page.

Or combinations. The old days of extension conflicts can be 2- and 3-way.

FWIW I just have Netgear GEnie and is okay, on 10.6.8 though.